Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3396

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 25247
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:11937 original size:6 final size:6

Alignment explanation


    Indices: 11926--11956  Score: 62
    Period size: 6  Copynumber: 5.2  Consensus size: 6

      11916 CTGATTGCAT

                                                
      11926 AGATGA AGATGA AGATGA AGATGA AGATGA A
          1 AGATGA AGATGA AGATGA AGATGA AGATGA A

      11957 ACCTCAAAGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16


Consensus pattern (6 bp):   
AGATGA

Found at i:16329 original size:50 final size:50

Alignment explanation


    Indices: 16274--16373  Score: 173
    Period size: 50  Copynumber: 2.0  Consensus size: 50

      16264 AGATTTATCA

                            *             *                   
      16274 CGGTAAAAGTACCATGGAGATCATTATATTTGACGGTAGATTTCATTTTG
          1 CGGTAAAAGTACCATGAAGATCATTATATTAGACGGTAGATTTCATTTTG

                                               *              
      16324 CGGTAAAAGTACCATGAAGATCATTATATTAGACGTTAGATTTCATTTTG
          1 CGGTAAAAGTACCATGAAGATCATTATATTAGACGGTAGATTTCATTTTG

      16374 TATGTTCTAT


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  50   47  1.00

ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36


Consensus pattern (50 bp):   
CGGTAAAAGTACCATGAAGATCATTATATTAGACGGTAGATTTCATTTTG

Found at i:18608 original size:22 final size:22

Alignment explanation


    Indices: 18580--18626  Score: 76
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      18570 AAACATACAT

                         *        
      18580 CCTAGGTGCCTAAGCAATGTAC
          1 CCTAGGTGCCTAACCAATGTAC

                    *             
      18602 CCTAGGTGTCTAACCAATGTAC
          1 CCTAGGTGCCTAACCAATGTAC

               
      18624 CCT
          1 CCT

      18627 CATTGATACC


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26


Consensus pattern (22 bp):   
CCTAGGTGCCTAACCAATGTAC

Found at i:19338 original size:39 final size:39

Alignment explanation


    Indices: 19295--19435  Score: 153
    Period size: 39  Copynumber: 3.6  Consensus size: 39

      19285 AAAACACACC

                            *             *        
      19295 AATTTGACACCCAGTGCCTCATCGGATAATTGAAGTAAT
          1 AATTTGACACCCAGTGTCTCATCGGATAATCGAAGTAAT

                                     *    *         
      19334 AATTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-
          1 AATTTGACACCCAGTGTCTCATCGGAT-AATCGAAGTAAT

                       *            *        *     * 
      19372 AA-TTGACACCTAGTGTCTCATCGAATTAATCCAAAGTAGT
          1 AATTTGACACCCAGTGTCTCATCGGA-TAAT-CGAAGTAAT

              *                     
      19412 AAATTGACACCCAGTGTCTCATCG
          1 AATTTGACACCCAGTGTCTCATCG

      19436 ACTCGAAGTC


Statistics
Matches: 85,  Mismatches: 11, Indels: 10
        0.80            0.10        0.09

Matches are distributed among these distances:
  37   22  0.26
  38    8  0.09
  39   26  0.31
  40    9  0.11
  41   20  0.24

ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27


Consensus pattern (39 bp):   
AATTTGACACCCAGTGTCTCATCGGATAATCGAAGTAAT

Found at i:19387 original size:37 final size:39

Alignment explanation


    Indices: 19337--19436  Score: 123
    Period size: 41  Copynumber: 2.6  Consensus size: 39

      19327 AAGTAATAAT

                                  *                
      19337 TTGACACCCAGTGTCTCATCG-GCTAAACC-GAAGTAAA
          1 TTGACACCCAGTGTCTCATCGAACTAAACCAGAAGTAAA

                    *              *   *      *      
      19374 TTGACACCTAGTGTCTCATCGAATTAATCCAAAGTAGTAAA
          1 TTGACACCCAGTGTCTCATCGAACTAAACC--AGAAGTAAA

                                  
      19415 TTGACACCCAGTGTCTCATCGA
          1 TTGACACCCAGTGTCTCATCGA

      19437 CTCGAAGTCG


Statistics
Matches: 53,  Mismatches: 6, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  37   20  0.38
  38    5  0.09
  41   28  0.53

ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26


Consensus pattern (39 bp):   
TTGACACCCAGTGTCTCATCGAACTAAACCAGAAGTAAA
Done.